Visual Materials

Chemical Structures

Chemical structures can be represented visually in a variety of ways. Therefore, it is important for readers to have mental flexibility when describing chemical images.

For example, the following three images express the same structure (adenosine triphosphate):ATP-xtal-3D-ballsAtp_exp.qutemol-ball2000px-Adenosintriphosphat_protoniert.svg

Each structure uses different visual cues to express the same information. I and my readers quickly get used to thinking about and describing structures in different ways. Sometimes colors are most pertinent, sometimes sizes, sometimes letters and line shading. With  large or complex structures, it is often important to be able to describe the same figure in different ways, approaching it repeatedly from different angles until all the descriptions synergies in my mind and give me a well-formed, comprehensive image.

Generally to begin approaching a unfamiliar structure, I have the reader identify the longest chain of repeating components, and then describe what branches off from this chain. This can work very well for organic compounds, but it is not always useful. It is always important to follow the logic of the molecule. If there is a central ring structure, begin with that and describe what branches out from it in a clockwise progression. If there isn’t a clear central pattern, I usually ask them to describe everything working from the left  to the right.

For large and complex structures, it can become difficult to keep track of details all the way through to the end of a long verbal description. Sometimes it helps me to write information down, even thought I can’t see what I’m writing. This is how my brain works. Another thing that helps is getting the general shape first, and then coloring it in with details. Often I will ask readers to trace the general shape of the molecule or compound onto the back of my hand or arm, and then to touch the part of the figure they are describing in detail. It gives me a frame of reference to hang newer details upon.

It is most convenient when my readers know the names of organic substituents. If they know chemical nomenclature, all the better. If they do not (or if they have any uncertainty) I expect them simply to name exactly what they see, atom by atom and bond by bond. In some cases, I might ask my readers to do some “homework,” aka. to memorize the names of certain common structures and chemical substituents. Being able to begin a description with, “It’s a phospholipid,” or “It’s a polysaccharide,” can streamline the process a lot. When readers know chemical terminology, it also makes it much easier for me to ask questions about pertinent information.

Complex Protein Structures

My graduate thesis focussed on HP urease, an enzyme with approximately 148,000 atoms. This massive system is difficult for a sighted person to analyze, let alone a blind individual. One of the techniques I used was detailing motion in terms of distance, deviations, and radial distributions between set residue pairs, as shown below in Figure 3. Mapping movement mathematically allowed me to ask the readers very concrete questions. It became a matter of accessing data mathematically, rather than in a complex visualization with lots of extraneous, distracting visual factors.

I would ask the readers to describe any general trends: for example, the green line has a steep upward climb from 100 to 200 ns. This is a mathematical approach to understanding molecular motion that avoided visual dependence and instead utilized a reader’s detailing of minima, maxima, plateaus and other features on a Cartesian plot.  Mathematical approaches like this are often a good alternative for visually-impaired researchers, and can, as in the case of my project, lead to unique discoveries that sighted students pass over.

Figure 3 See Alternative Visualizations for more information on performing research on complex protein structures.

Mathematical Equations

Accurate, fluent verbal expression of mathematical equations is not a common skill, even in people who specialize in math and science. Therefore I often do a bit of training for my readers. To begin, I make sure they memorize the greek alphabet, learn the proper terminology, and know the correct order to read each of the phases in a long equation.  Some instructions that I give them are very simple. For example, I ask them to make sure they name brackets and parentheses correctly. There are many such details that a sighted person breezes over because they are used to reading and writing math, not speaking it. Once I am confident about a readers ability, I might also assign them to record the equations in the articles/chapters to be added to to my library of recordings.

I have mathematical expressions recorded separately from the main body the text and saved in a separate file within the larger folder. It is helpful to have equations quickly accessible, rather than having to listen through the entire paper/chapter.

Terminal

A computer terminal can be thought of as the portal to all the inner workings of the computer. It’s a different way to see the information in your computer. Rater than image based, it’s text based. You can use it to maneuver through the computer’s folders and files via typed commands, rather than a cursor.

As a computational chemist, I spend a lot of time working within the terminal. A lot of my maneuvering through the terminal depends on my memory of the organization scheme of each folder and file. Currently, I have a reader with a background in coding who works alongside me. We work through problems together, with him to describe that which I cannot read. He also takes commands from me, because in same cases his sight allows him to enact them more quickly.

Plots

When my reader and I come upon a plot, I always start by having them define the x and y axes, and then I have them trace the general shape of the lines on the back of my hand, starting in the bottom left corner of the plot. From here, I ask if there are any patterns or distinctive features. I ask if there is a maximum, if there is a minimum, if the lines form a curved shape or a parabola.

There have been cases where I missed something critical in a plot because the reader did not describe it to me. When this happens, it is not their fault but mine. It is my responsibility to get better at knowing which questions to ask to extract the information I need.